Length of the merged reads (merged reads over 300pb).
Not enough overlaping when merging the paired reads.
Use other pre-cluster algorithm like Deblur.
Too many uniques?
Not enough computer power?: Use HPC or Cluster.
Try to make contigs using maxee instead of deltaq or use phylogeny
approach for downstream analysis, or use clister.split based on
taxonomy.
do not forget to use controls.
References
1. Weißbecker, C., Schnabel, B., & Heintz-Buschart, A. (2021).
Dadasnake, a snakemake implementation of DADA2 to process amplicon
sequencing data for microbial ecology. GigaScience, 9.
https://doi.org/10.1093/gigascience/giaa135